query_enrichr_py*.py : python scripts to programmatically enrich your data using Enrichr
Note: all credit goes to the Enrichr folks...I just stuck their examples from http://amp.pharm.mssm.edu/Enrichr/help#api together
BMC Bioinformatics. 2013 Apr 15;14:128. doi: 10.1186/1471-2105-14-128
[PMID: 23586463 [PubMed - indexed for MEDLINE] PMCID: PMC3637064] (http://www.ncbi.nlm.nih.gov/pubmed/23586463)
Enrichr, ia an integrative web-based and mobile software application that includes new gene-set libraries, an alternative approach to rank enriched terms, and various interactive visualization approaches to display enrichment results using the JavaScript library, Data Driven Documents (D3). The software can also be embedded into any tool that performs gene list analysis. Enrichr is an easy to use intuitive enrichment analysis web-based tool providing various types of visualization summaries of collective functions of gene lists.
Enrichr is open source and freely available online at: http://amp.pharm.mssm.edu/Enrichr .
git clone https://github.com/snewhouse/enrichr-api.git python query_enrichr_p2.py <genelist> <listdesrciption> <enrichr_library> <enrichr_results>python query_enrichr_p3.py <genelist> <listdesrciption> <enrichr_library> <enrichr_results>Positional Inputs
- genelist : flat file with list of genes, one gene id per row
- listdesrciption : name of analysis
- enrichr_library : Enrichr Library to query. See below.
- enrichr_results : out put file prefix
- python
Tested with Python 2.7.11
Tested with Python 3.5.1 :: Anaconda 4.0.0 (x86_64)
Query KEGG_2015
Input Options:
- genelist : gene_list.txt
- listdesrciption : my_test
- enrichr_library : KEGG_2015
- enrichr_results : KEGG_2015__enrichment
The code
## run it
python query_enrichr_p3.py gene_list.txt my_test KEGG_2015 KEGG_2015__enrichment